I've had this happen several times, and I almost exclusively use Tamiya paint. The paint seems to 'orientate' itself with the swirl marks in the raw plastic. Not sure of a solution, but i have tried these two methods with varying degrees of success:
1) Try building up the paint in mist coats. This sometimes solves the problem, but beware heavy clear coats afterwards.
2) Strip the paint from a smaller part, and sand the raw pastic with fine sandpaper. Repeat the painting process (light coats) and see if this works. If it does, the good news is you have solved the problem - bad news, you have to repeat on all the other parts .
Good luck